Joi Ito's Web

Joi Ito's conversation with the living web.

Recently in the MIT Media Lab Category

Darren Walker and the Ford Foundation threw a book party for my new book Whiplash (Thanks!) and Megan came a bit early so I got a chance to sit down with her and do a Facebook Live. Megan is the former CTO of the United States serving under President Obama. She's an MIT grad, did her thesis work at the Media Lab, is on the corporation board of MIT and the advisory council and visiting committee of the Media Lab. She's also the one who first asked me whether I wanted to be considered for the role of the Director of the Media Lab so I owe a lot to her. I've known Megan for a long time and it was great catching up.

We talked about tech, digital government, inclusion and the opportunities ahead.

The audio is available on iTunes and SoundCloud.

I recently had a Facebook Live conversation with Shaka Senghor, a Media Lab Director's Fellow and author. Shaka spent 19 years in prison for second-degree murder. In prison Shaka found a path to redemption initially through reading and then writing. I met him just after he had come out of prison. You can read more about this in the foreword to his book that I wrote.

Shaka's an amazing leader, writer, inspiration and an important voice behind the fight against the systematic mass incarceration in the US.

We talk about prison, his book, Writing My Wrongs and a bit about Whiplash.

Audio of the conversation is available on iTunes and SoundCloud.


Neha Narula wrote a post on Medium last Monday about the MIT Digital Currency Initiative at the Media Lab (DCI) and her new role as the Research Director. Also on Monday, TED posted her talk on the future of money, which I think is one of clearest "what is Bitcoin" explanations I've seen. I saw her a few days later and did a Facebook Live conversation with her which I've uploaded to YouTube, SoundCloud and iTunes.

Neha has been working as a member of the DCI for awhile now, but in this new role, she will drive the technical research agenda of the DCI and help coordinate research inside of MIT as well as in other academic institutions and in the broader community. She comes with a solid technical background with a PhD from MIT in distributed systems and previously as a software engineer at Google. Neha and the DCI have already been actively engaged in research, development and teaching in digital currencies, blockchain and related fields, but with Neha's leadership, I'm hoping that we can continue to ramp these efforts up as well as increase collaboration and engagement.

Neha lead the creation of a website for the DCI where you can learn about some of the projects and people involved. Also, as I wrote in a Medium post on September 6, Brian Forde, the director of the DCI will be transitioning out of that role.

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Photo by Daderot [Public domain], via Wikimedia Commons

When I was first appointed as the director of the MIT Media Lab, The New York Times said it was an "unusual choice" - which it was since my highest academic degree was my high school diploma, and, in fact, had dropped out of undergraduate programs at both Tufts and the University of Chicago, as well as a doctoral program at Hitotsubashi University in Tokyo.

When first approached about the position, I was given advice that I shouldn't apply considering my lack of a degree. Months later, I was contacted again by Nicholas Negroponte, who was on the search committee, and who invited me to visit MIT for interviews. Turns out they hadn't come up with a final candidate from the first list.

The interview with the faculty, student and staff went well - two of the most exciting days of my life - although quite painful as well, as a major earthquake in Japan occurred the night between the two days. In so many ways, those two days are etched into my mind.

The committee got back to me quickly. I was their first choice, and needed to come back and have meetings with the School of Architecture + Planning Dean Adele Santos, and possibly the provost (now MIT president) Rafael Reif, since I was such an unorthodox candidate. When I sat down to meet with Rafael in his fancy office, he gave me a bit of a "what are you doing here?" look and asked, "How can I help you?" I explained the unusual circumstance of my candidacy. He smiled and said, "Welcome to MIT!" in the warm and welcoming way he treats everyone.

As the director of the Media Lab, my job is to oversee the operations and research of the Lab. At MIT, the norm is for research labs and academic programs to be separated-like church and state-but the Media Lab is unique in that it has "its own" academic Program in Media Arts and Sciences within the School of Architecture + Planning, which is tightly linked to the research.

Since its inception, the Lab has always emphasized hands-on research: learning by doing, demoing and deploying our works rather than just publishing. The academic program is led by a faculty member, currently Pattie Maes, with whom I work very closely.

My predecessor, as well as Nicholas, the lab's founding director, both had faculty appointments. However, in my case, due to the combination of my not knowing any better and the Institute not being sure about whether I had the chops to advise students and be sufficiently academic, I was not given the faculty position when I joined.

In most cases, it didn't matter. I participated in all of the faculty meetings, and except for rare occasions, was made to feel completely empowered and supported. The only awkward moments were when I was mistakenly addressed as "Professor Ito," or after explaining my position to academics from other universities had to endure responses like, "Oh! I thought you were faculty but you're on the ADMINISTRATIVE side of the house!"

So I didn't feel like I NEEDED to be a professor. When I was offered the opportunity to submit a proposal to become a professor, I wasn't sure exactly how it would help. I asked a few of my mentors and they said that it would allow me to have a life at MIT after I was no longer Lab director. Frankly, I can't imagine ever leaving my role as director of the Lab, but that was a nice option. Also, becoming a professor makes me more formally part of the Institute itself. It is a vote of confidence since it requires approval by the academic council.

I am not interested in starting my own research group, but rather have always viewed the entire Media Lab itself my "research group," as well as my passion. However, as I help start new initiatives and support faculty, from time to time, I have become more involved in thinking and doing things that require a more academic frame of mind. Lastly, I have begun to have more opinions about the academic program at the Media Lab and more broadly at MIT. Becoming a faculty member would give me a much better position from which to express these opinions.

With these thoughts in mind-and with advice from my wise mentors-I requested, and today received, appointment as a member of the MIT faculty, as a Professor of the Practice in Media Arts and Sciences.

I still remember when I used to argue with my sister, a double PhD, researcher, and faculty member, calling her "academic" as a derogatory term. I remember many people warning me when I took the role as the director of the Media Lab that I wouldn't fit in or that I'd get sick of it. I've now been at MIT approximately five years - longer than I've been at any other job - (and my sister, Mimi, is now an entrepreneur.) I feel like I've finally found my true calling and am happier than I've ever been with my work, my community and the potential for growth and impact for myself and the community in which I serve.

So thank you MIT and all of my mentors, peers, students, staff, and friends who have supported me so far. I look forward to continuing this journey to see where it goes.

I've posted the research statement that I submitted to MIT for the promotion case.

The appointment is effective July 1, 2016.


On Sunday, I tried convening a conversation with Media Lab students and researchers to have an open conversation where we streamed it live on Facebook and YouTube. We ended up talking a lot about communications, ideas and patents. I got mostly positive feedback so I think we'll do it again. Any thoughts on how to improve the format would be greatly appreciated.

Better audio and video is on the list.

Conversation at the MIT Media Lab about cybernetics with Paul Pangaro, Nathan Felde, Mike Bove, Iyad Rahwan, Edith Ackermann, Joi Ito and Lorrie LeJeune. A few background posts: http://jods.mitpress.mit.edu/pub/designandscience / http://www.dubberly.com/articles/cybernetics-and-counterculture.html - March 17, 2016 - noon - 1:30PM Eastern Time

We posted it live on Facebook using FB Mentions and the archive of the video and the chat are up there now.

As an experiment, I also uploaded to YouTube and embedded it below. If you have the energy, please try both and tell me which you like better.

More broadly, this is an experiment in video but also in "fly on the way" streaming. Please let me know if you find this interesting. Trying to decide whether to do more of it and whether to do it on FB, YouTube, Periscope or some other platform.

Also, other than a better lens and a better mic, what can I do to improve it?

Kevin Esvelt accepted our offer and will be joining us in January as an assistant professor heading his new Sculpting Evolution research group.

Kevin is a Harvard-trained biologist who is merging some of the newest techniques in molecular biology with ecological engineering. He contributed to the development of the CRISPR/Cas9 gene editing technology, and was responsible for revealing the possibility of CRISPR gene drives. CRISPR gene drives allow us to edit the genomes of existing organisms and force all subsequent offspring to inherit the alteration. This could, for instance, allow us to release mosquitoes into the wild and over time eliminate the ability for the populations of wild mosquitoes to carry malaria, dengue, or other diseases. Other possible applications include eliminating Lyme disease by permanently immunizing the mice who transmit the disease to ticks, eradicating the blood fluke parasite responsible for schistosomiasis, and even alleviating the need for harmful pesticides by programming pests so they do not want to eat our crops.

As you might imagine, there is a tremendous amount of upside, but also quite a bit of fear and some real risks. One of the key things that Kevin is working on, in addition to figuring how we might deploy these technologies, is to develop safety technologies to ensure that laboratory accidents don't affect the environment as well as an "undo" version that could be released if we wanted to revert the edit.

Kevin and George Church published the first papers on CRISPR gene drives even before starting experiments because they wanted to set a precedent that conversations on responsible use should start early. One of the key things about CRISPR is its low cost - add CRISPR gene drive, and the number of bio facilities able to release potentially world-changing alterations will only grow with time.

At the Media Lab's 30th anniversary event this past October, Kevin asked the audience, "Who should decide?" Who can responsibly make the decision whether we should release these mosquitos and potentially eliminate malaria or allow us to reduce the tons of pesticides we are using, knowing that at the same time we will risk altering our ecosystem in irreversible ways? In a country where the majority of people don't believe in evolution and where we have a Congress that can't even get behind the idea that climate change is a critical issue, it's a hard question.

At our secret meeting with JJ Abrams, Kevin explained that we not only need to decide how to deal with world-changing new science like CRISPR and gene drive, but that we also need to prepare ourselves for a world where the rate at which these world-changing sciences are discovered continues to increase. It is critical for us to understand how to responsibly make decisions as society and as scientists.

We hope that the Media Lab can play a critical role in the discovery of these new technologies, the discussion around their impact, as well as the responsible design and deployment of them. We believe that design in the context of science provides reflection and ethical considerations at a fundamental level. No one discipline should ever be developed in isolation from the many other lenses on the world; the Media Lab has held this as a guiding principle for 30 years. As this new science around gene editing comes online, we are happy it does so here, where science is bound to design, much as it is in Esvelt himself.

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Announcement on MIT News and crossposted on the MIT Medium Blog.

I am proud to announce that we have offered Bassel Khartabil a position as a research scientist in the Center for Civic Media at the MIT Media Lab, where he will work directly with its director, principal research scientist Ethan Zuckerman. As a research scientist at the Media Lab, Bassel will be able to continue his longstanding work protecting spaces for online speech-work that fits naturally with the core research mission of the Center. In particular, Bassel is currently working on reconstructing in 3D the ancient ruins of Palmyra, one of the sites raided and destroyed by ISIS.

Bassel Safadi

Bassel Khartabil is a dear friend and former colleague at Creative Commons, and a vocal and brilliant advocate and worker for free culture on the Internet. Bassel invited me to Damascus in 2009 and introduced me to students, artists, and Syrian culture, and it remains the most inspiring trip I've ever made in the region. While I was there, he took me to visit ancient Roman sites as well as arranging a wonderful dinner with local tech entrepreneurs. The relationship between history, arts, and technology was stunning-something that no other city does as elegantly as Damascus. (Here are some of my photos from the trip.)

On March 15, 2012, Bassel was arrested by the Syrian military police, and eventually tried without a lawyer present at a military field court. Advocates across the globe have challenged his arrest and detention, arguing that his work presented no threat to anyone inside or outside of Syria, and instead represented the best aspirations of the open software movement.

I am writing this post now because, along with his family, friends, and colleagues around the world, I am very concerned about Bassel's safety. Until recently, he has been held at Adra Prison, but his current whereabouts are unknown-as of yet the Syrian government has not shared any information about where he is or why he was moved.

Bassel has devoted his career to the rich culture of Syria and to protecting that culture. His contributions to the open Internet and open culture internationally, and his research and creativity, have benefitted all of us. Without people like Bassel, the Internet wouldn't be the vibrant and open resource that many of us take for granted.

Stéphanie Vidal has written a detailed and thoughtful piece about Bassel's situation for Slate.fr, and Creative Commons has published a translation by Philippe Aigrain, Mélanie Dulong de Rosnay, and Jean-Christophe Peyssard on their blog. I encourage you to read these to understand the intricacies of Bassel's situation. One part of Stéphanie's essay in particular really stood out for me:

When there is no longer respect for human rights, public calls can only state what one hopes for. This brings us to the second point: the more the affirmation of our hope is shared and present on the Web and social media, the more it may turn to a reality. Bassel's engagement in favor of a free Internet may have brought him to jail, but the attention that we, citizens on the Internet, give to this case may, to some degree, help bring him out of the darkness.

In the name of the international academic community, I would like to ask President Assad to please give Bassel Khartabil a presidential pardon. He is an important world citizen and a true Syrian trying to protect the heritage of the country, and a pardon would be a tremendous show of good will and a contribution to the preservation of Syrian culture.

Please share this post widely and keep Bassel in your thoughts.

Links:

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As Bitcoin continues to gain momentum and capture the interest of entrepreneurs, hackers, businesses, policymakers, and academics, we have decided to launch an Initiative at the MIT Media Lab, with participation from faculty and students from across the Institute, focusing on Bitcoin and more generally cryptocurrencies.

The Initiative will explore vital research topics that our faculty and students will engage in with the support and participation of some Media Lab member companies. The students running the MIT Bitcoin Club, the MIT Bitcoin Project, and the various events including the Bitcoin Expo have been a key part of getting this initiative started. The MIT Bitcoin Expo, which was hosted by MIT Bitcoin Club President Jonathan Harvey-Buschel and Wellesley Bitcoin Club President Jinglan Wang this year exemplified the kind of interscholastic collaboration and excitement over Bitcoin research that we want to see going forward.

The Media Lab has hired former White House senior advisor for mobile and data innovation, Brian Forde to lead the overall effort along with MIT CSAIL's Nickolai Zeldovich, a highly distinguished professor in security and distributed systems, who will be coordinating the research and academics. Jeremy Rubin, an undergraduate who helped run the MIT Bitcoin Project, will coordinate communications with the broader developer community and MIT students and will also work on research projects. More details on other MIT participants can be found in Brian's blog post.

The Initiative's focus will be heavily informed by the work done by the Bitcoin community, as well as by companies and forward-thinking policy makers. We hope to be able to contribute academically and technically to the field, following the great example set by Princeton and others. This is more about rallying interest within the MIT community than forming a general long-term solution for Bitcoin development and governance.

As I've said in a previous blog post and my talk at the MIT Bitcoin Expo, I do think there is a real need for a coordinating function around standards and policy. I believe that this effort must be multinational and multistakeholder. Continuing discussion with the Berkman Center at Harvard, Stanford Center for Internet and Society, and Oxford University will, we hope, contribute to the broader conversation on this matter.

See the post by Brian on the Media Lab blog for more information about the Initiative. We've set up an IRC channel irc.freenode.net/#mit-dci, where we will be hanging out. We look forward to your feedback and ideas for collaboration.

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One of the first words that I learned when I joined the Media Lab was "antidisciplinary." It was listed an a requirement in an ad seeking applicants for a new faculty position. Interdisciplinary work is when people from different disciplines work together. An antidisciplinary project isn't a sum of a bunch of disciplines but something entirely new - the word defies easy definition. But what it means to me is someone or something that doesn't fit within traditional academic discipline­­­-a field of study with its own particular words, frameworks, and methods. Most academics are judged by how many times they have published in prestigious, peer-reviewed journals. Peer review usually consists of the influential members of your field reviewing your work and deciding whether it is important and unique. This architecture often leads to a dynamic where researchers focus more on impressing a small number of experts in their own field than on taking the high risk of an unconventional approach. This dynamic reinforces the cliché of academics-learning more and more about less and less. It causes a hyper-specialization where people in different areas have a very difficult time collaborating-or even communicating-with people in different fields. For me, antidisciplinary research is akin to mathematician Stanislaw Ulam's famous observation that the study of non-linear physics is like the study of "non-elephant animals." Antidisciplinary is all about the non-elephant animals.

The Media Lab focuses on "uniqueness, impact and magic." What our students and faculty do should be unique. We shouldn't be doing something that someone else is doing. If someone else starts doing it, we should stop. Everything we do should have impact. Lastly, things should induce us to be passionate and should go beyond incremental thinking. "Magic" means that we take on projects that inspire us. In the Lifelong Kindergarten group, researchers often describe the "Four Ps of Creative Learning" as Projects, Peers, Passion and Play. Play is extremely important for creative learning. There is a great deal of research showing that rewards and pressure can motivate people to "produce," but creative learning and thinking requires the "space" that play creates. Pressure and rewards can often diminish that space, and thus, squash creative thinking.

The kind of scholars we are looking for at the Media Lab are people who don't fit in any existing discipline either because they are between--or simply beyond--disciplines. I often say that if you can do what you want to do in any other lab or department, you should go do it there. Only come to the Media Lab if there is nowhere else where you could do what you want to do. We are the home of the misfits-the antidisciplinarians.

When I think about the "space" that we've created, I like to think about a huge piece of paper that represents "all science." The disciplines are little black dots on this paper. The massive amounts of white space between the dots represent antidisciplinary space. Many people would like to play in this white space, but there is very little funding for this, and it's even harder to get a tenured positions without some sort of disciplinary anchor in one of the black dots.

As we engage in tackling harder and harder problems that require many fields and perspectives, the separation of disciplines appears to be causing more and more damage. The complex system that is the human body has become impossibly multi-disciplinary. We should really be working on "One Science," but instead we are a mosaic of different disciplines sometimes not even recognizing when we are looking at the same problem because our language is so different and microscopes are set so differently.

The Center for Extreme Bionics at the Media Lab--led by Hugh Herr, Ed Boyden, Joe Jacobson, and Bob Langer--utilizes everything from mechanical engineering to synthetic biology to neuroscience in its quest to eliminate a variety of disabilities. This disparate collection of disciplines would never fit in any traditional department or lab.

Media Lab co-founder Nicholas Negroponte famously coined a twist on the academic dictum that faculty must "publish or perish." Media Lab faculty, he said, must "demo or die." I have made a modification- "Deploy or die." I'd like all of the Lab's faculty and students thinking about how their work ultimately deploys in the world, and if they can deploy it themselves, even better.

I think this philosophy of working together on big projects will help bring researchers together across disciplines - creating a single science instead of fragmented disciplines. We will still need disciplines, but I think that it's time we focus on a higher mission and the changes needed in academia and research funding to allow more people to work in the wide-open white space between disciplines - the antidisciplinary space.

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Update: One of our faculty members pointed out that disciplines are more like broad swaths and that a lot of the most cited papers are the ones in the disruptive "antidisciplinary" spaces.

I first heard about Synbiota at SXSWi this year, when they won an Accelerator Award. According to the announcement, "Synbiota is a virtual collaboration site that connects scientists, researchers, universities and others from around the world to solve complex problems using genetic engineering." That week they announced the world's first Massive Open Online Science (MOOS) event. Called #ScienceHack, hundreds of researchers from around the globe (some as clueless as us!) would use a new "wetware" kit to produce prohibitively expensive medicine at a fraction of the price.

A month later I got this email:

From: Connor Dickie
To: Joi Ito
Cc: Kim de Mora
Date: Apr 17, 2014, at 11:12
Subject: ML alumni wins SXSW prize for SynBio startup & Invitation to #ScienceHack

"I'm writing to invite you to participate in #ScienceHack, our distributed science effort to make real medicine for just a fraction of current costs using Synthetic Biology and the Synbiota platform. O'Reilly Radar recently called #ScienceHack the most ambitious distributed science project, and knowing your interest in biotech, I thought I'd reach out to you with a cool opportunity to learn with us.

Participation is easy - I'll ship you one of our "Violacein Factory" wetware kits, and connect you with Kim de Mora at iGEM HQ (CC'd) who is not only interested to build one of the kits, but also has the required wet lab skills. It will take about an hour and a half for the in-silico design and build of the actual DNA part. Kim would handle the incubation etc. You would then come back to his lab in about 5 days to look at the results.

We recently built a Violacein Factory kit here in Canada, and more recently at Genspace in NYC, and everyone learned a bunch and helped us make significant advances towards our goal of an optimized violacein-producing organism.

I'll be in Boston/Cambridge on the 27th-through-30th as part of a Canadian trade delegation, and will have some time to meet you and chat about the opportunity in person if it interests you.

With regards,

Connor Dickie
http://alumni.media.mit.edu/~connord/

I knew about iGEM. It was the spinout from MIT that brought high school and college students together to hack DNA much in the same way that robot competitions bring together kids interested in robots to hack and learn and compete. What's amazing is that iGEM, now bringing together over two thousand students at their Jamboree, takes the state of the art of synthetic biology and brings it to the masses.

Violacein is a natural purple compound made by Chromobacterium violaceum, a bacteria that is found in the soil in the tropics such as the Amazon. Violacein is created by the bacteria as a natural defense against amoebic creatures that try to eat it and is viewed as a potential anti-parasitic. It also appears to show promise as a treatment for cancer. The problem is that it currently costs $356,000 per gram because of the difficulty of harvesting it in the wild.

An opportunity to learn synthetic biology through doing it (my favorite way to learn) was too good to turn down so I immediately accepted the challenge. I started by taking the required safety courses for playing with recombinant DNA : General Biosafety for Researchers, check. Bloodborne Pathogens: Researchers, check. Hepatitis Information form, check. General Chemical Hygiene (web) and Managing Hazardous Waste (web). Check and check.

Then I started hunting for a place to do the actual work. That turned out to be a bit more of a challenge. Although the kit and process provided by Synbiota were basically safe and non-toxic, work with recombinant DNA and bacteria required a proper wet lab at MIT which are in short supply and used for more important things than the Media Lab director messing around with street bio.

After discussing with the team and looking at what we needed, we decided that my kitchen would be the least disruptive place to do the work.

On July 27, the Synbiota team and Kim from iGEM gathered at my house with a rag tag team of researchers from the Media Lab and elsewhere to work on the Violacein Factory #Sciencehack. We started with a briefing on what we were actually doing.

Our mission was to be one of the hundreds of teams participating in trying to innovate on developing the most effective method of synthesizing Violacein using synthetic biology.

Scientists have determined the metabolic pathway in Chromobacterium violaceum that converts tryptophan, a common amino acid, into violacein. This pathway involves five enzymes and various genetic sequences for their production. These "parts" of genetic code can be positioned differently in the DNA molecule and each combination has different attributes and tradeoffs - the optimal sequence and combination being currently unknown.

Synbiota kit parts

The #ScienceHack Violacein Factory Kit co-designed with Genomikon which develops synthetic biology kits, had vials of all of the various genetic "parts" and the other materials needed to assemble these parts into a plasmid. According to Synbiota:

This Kit includes everything you need except:

• pipettes, nitrile gloves, petri dishes, PCR tubes, lab coats (for the full biotech experience, but any ol' trench coat will do!)
• ice buckets and ice
• 42 C water bath with epi tube floaty blanket
• 37 C incubator

All the above can be found around the house, from online suppliers, at your local university lab store, or in a friendly scientist's stash.

Kim from iGEM brought everything from the iGEM lab. He walked us through the kitchen version of the protocol for using all of the equipment safely.

Synbiota, in addition to putting together this amazing #ScienceHack project has developed a suite of online tools to publish and share lab books online (I guess I don't need that fancy paper notebook I bought!), design DNA using a very nice graphical interface and provide researchers with a whole suite of tools to do synthetic biology as a community. Everything was very well designed and worked well.

First, I created an account on the Synbiota website and logged into our notebook. Justin explained the violacein pathway and explained how we can use the online gene editor, GENtle3, (video) to design the gene sequence online.

In GENtle3, we were able to drag and drop any of the genetic parts that came in the kit into our sequence and as long as we followed the basic rules of which parts could be connected to each other. The sequence I designed was Anc-ABEDDDC-Cap, where A, B, C, D, E represent the enzymes that make up the violacein metabolic pathway. (Visit the sequence tab in the Sciencehack project to view this and other designed sequences.)

The sequence had to start with the Anchor--Origin-X' part because that was the part that was attached to the magnetic bead. One of the keys to being able to do all of this amazing work in a kitchen had to do with this innovation.

In the kit were tiny sub-micron magnetic beads with the anchor part - a strand of DNA attached to it. What this meant is that we could use a small but very strong external magnet held to the side of the container - the epi tube - to pull all of the genetic material we were working with to the side of the epi tube allowing us to insert and extract liquids from the container using pipettes while leaving our working material secured to the container.

What we needed to do after designing our sequence was to assemble it. We did this putting the beads in a epi tube, adding a "wash", removing the wash, adding a genetic part from a color coded tube that corresponded with the next link in our design, adding the T4 DNA ligase, the "genetic glue" to attach that new part to the strand on the bead, removing the excess material, washing again, and then repeating until we had added each part in order to the bead. Theoretically, we should now have a long strands of DNA attached to each bead representing our version of the DNA sequence (plasmid) that we designed.

The last step was to use a buffer to remove the bead from the strands and we had a little drop of genetic material that when inserted into a living bacteria should create all of the enzymes necessary to produce violacein from tryptophan.

The next step was what was called "transformation" which is the process that takes our plasmid and inserts it into a bacteria, in our caseE. coli. The "competent" E. coli designed for easier transfection were created at iGEM. The process we used for transformation was called "heat shock" which involved adding our genetic material to a salt solution with the E. coli and then rapidly heating it which caused the genetic material to be absorbed into the E. coli. The device used for heating, I noticed, had a sticker from the "MIT Property Equipment Office" on it. Definitely a bit punk rock. After the "shock" we added liquid material with nutrients and minerals that "rebooted" the E. coli, waking it up and preparing it to be incubated for execution of the DNA code we just inserted.

The E. coli were then spread onto petri dishes with Jello-like "food" as well as an antibiotic, chloramphenicol. The chloramphenicol would kill all other bacteria on the dish except our own because we had cleverly included a chloramphenicol resistance building genetic part in our sequence.

Heat shocker

We then sent the petri dishes back to iGEM for incubation. The results were not perfect, but none-the-less, it looks like violacein and other molecules from the pathway were created (some other got different colours). The images of my petri dish show a kind of blackish zig-zag smear which are billions of bacteria producing metabolites because the executed DNA I designed and created. At this point I don't know for sure whether violacein was created - I need to do more verification and experimentation, but for a first go at building a complex metabolic pathway, not too shabby. Something else that is cool, is that my intended DNA design was very long, 12,000 base pairs, the next #ScienceHack step is to verify that the entire code I designed was actually assembled properly. We shared our designs, protocols and procedures with the rest of the teams. The next step was to look at the work of the other teams and try to find out what we could improve and try again.

In two half days of work, we were able to do in our kitchen what would have been Nobel Prize winning work a decade ago. We designed a sequence of genes, actually assembled the genes and then injected them into a bacteria and rebooted the bacteria.

Also, unlike traditional labs where one team would do the work and publish a paper and then other teams would try to replicate the work, we worked as one large team of parallel labs sharing our work as we went along, iterating, innovating and discussing.

I think that there is a good chance that one of the hundreds of teams will discover an efficient way of synthesizing, extracting, and purifying violacein and that soon we will have something that will probably initially look something like a homebrew beer brewing contraption producing the extremely rare compound for researchers with instructions on how anyone can build one of these violacein factories.

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Disclosure : After this experience, I was so excited that I donated to iGEM and decided to invest in Synbiota.